[med-svn] [libseqlib] 04/04: Use Debian packaged ssw

[Andreas Tille]

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tille pushed a commit to branch master
in repository libseqlib.

commit c806b9e3e5d8f7b9cfa1aa5658c06d05ccc5031d
Author: Andreas Tille <tille at debian.org>
Date:   Fri Feb 3 22:12:50 2017 +0100

    Use Debian packaged ssw
---
 debian/patches/series                        |  1 +
 debian/patches/use_debian_packaged_ssw.patch | 34 ++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 3fe6273..a9f8c96 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ fix_htslib_usage.patch
 fml_include_path.patch
 dynamic_lib.patch
 use_debian_packaged_jsoncpp.patch
+use_debian_packaged_ssw.patch
diff --git a/debian/patches/use_debian_packaged_ssw.patch b/debian/patches/use_debian_packaged_ssw.patch
new file mode 100644
index 0000000..a495193
--- /dev/null
+++ b/debian/patches/use_debian_packaged_ssw.patch
@@ -0,0 +1,34 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
+Description: Do not use code copy of libssw
+
+--- a/seq_test/Makefile.am
++++ b/seq_test/Makefile.am
+@@ -17,4 +17,4 @@ seq_test_SOURCES = seq_test.cpp \
+ 	../src/ReadFilter.cpp ../src/BamRecord.cpp \
+ 	../src/BWAWrapper.cpp \
+         ../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
+-	../src/FermiAssembler.cpp ../src/ssw_cpp.cpp ../src/ssw.c
++	../src/FermiAssembler.cpp
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -2,7 +2,7 @@ lib_LTLIBRARIES  = libseqlib.la
+ 
+ libseqlib_la_CPPFLAGS = -I../ -I../htslib -I/usr/include/fml -I/usr/include/jsoncpp/ -Wno-sign-compare
+ 
+-libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp ssw_cpp.cpp ssw.c \
++libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp \
+ 			GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
+ 			BWAWrapper.cpp BamRecord.cpp FermiAssembler.cpp BamHeader.cpp
+ libseqlib_la_LDFLAGS = -version-info @LIB_VERSION@
+--- a/src/BamRecord.cpp
++++ b/src/BamRecord.cpp
+@@ -5,7 +5,7 @@
+ #include <cctype>
+ #include <stdexcept>
+ 
+-#include "SeqLib/ssw_cpp.h"
++#include <ssw_cpp.h>
+ 
+ #define TAG_DELIMITER "^"
+ #define CTAG_DELIMITER '^'

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